Human rhinovirus (HRV), the most common cause of upper respiratory infection in children, can present as bronchiolitis, pneumonia, or asthma exacerbations. The impact of HRV in infants and toddlers with congenital heart disease is poorly defined. A case-control study was performed to compare the clinical course for 19 young children with respiratory symptoms who tested positive for rhinovirus after heart surgery with that of 56 matched control subjects. The control subjects were matched by surgical repair, age, weight, and time of the year. Patients with known HRVs before surgery and control subjects with respiratory symptoms or positive test results for viruses were excluded from the study. Human rhinovirus infection was associated with more than a tenfold increase in the odds of noninvasive ventilation after extubation (odds ratio [OR] 11.45; 95 % confidence interval [CI] 3.97-38.67), a 12-fold increase in the probability of extubation failure (OR 12.84; 95 % CI 2.93-56.29), and increased use of pulmonary medications including bronchodilator and nitric oxide (p < 0.001). As a result, the hospital length of stay (HLOS) was two times longer than for the control subjects (p < 0.001), and the cardiac intensive care unit (CICU) length of stay (CICU LOS) was three times longer (p < 0.0001). The intubation time was significantly longer (p < 0.001), and the CICU respiratory charges were significantly greater (p = 0.001) for the infected patients. Human rhinovirus increases resource use and prolongs postoperative recovery after pediatric heart surgery. Surgery timing should be delayed for patients with rhinovirus if possible.